org.opencb.cellbase.lib.builders

Class RegulatoryRegionParser

java.lang.Object

org.opencb.cellbase.lib.builders.CellBaseParser

org.opencb.cellbase.lib.builders.RegulatoryRegionParser

public class RegulatoryRegionParser
extends CellBaseParser

User: fsalavert. Date: 4/10/13 Time: 10:14 AM

Field Summary

Fields inherited from class org.opencb.cellbase.lib.builders.CellBaseParser

logger, serializer

Constructor Summary

Constructors

Constructor and Description
RegulatoryRegionParser(Path regulatoryRegionFilesDir, CellBaseSerializer serializer)

Method Summary

Modifier and Type	Method and Description
void	createSQLiteRegulatoryFiles(Path regulatoryRegionPath)
void	createSQLiteRegulatoryFiles(Path filePath, String tableName, List<String> columnNames, List<String> columnTypes)
static List<String>	getAnnotatedFeaturesFields(String line) Deprecated.
List<String>	getChromosomesList(Path dbPath, String tableName)
static List<String>	getFields(String line, String tableName)
static List<String>	getMirnaFeaturesFields(String line)
static List<String>	getMotifFeaturesFields(String line)
static List<String>	getRegulatoryFeaturesFields(String line)
static void	insertByType(PreparedStatement ps, List<String> fields, List<String> types)
void	parse()
List<org.opencb.biodata.models.core.RegulatoryFeature>	queryChromosomesRegulatoryDB(Path dbPath, String tableName, String chromosome)
static List<org.opencb.biodata.models.core.RegulatoryFeature>	queryRegulatoryDB(Path dbPath, String tableName, String chrFile, int start, int end)
String	repeat(String s, int n)

Methods inherited from class org.opencb.cellbase.lib.builders.CellBaseParser

disconnect

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RegulatoryRegionParser

public RegulatoryRegionParser(Path regulatoryRegionFilesDir,
                              CellBaseSerializer serializer)

Method Detail

createSQLiteRegulatoryFiles

public void createSQLiteRegulatoryFiles(Path regulatoryRegionPath)
                                 throws SQLException,
                                        IOException,
                                        ClassNotFoundException,
                                        NoSuchMethodException

Throws:

SQLException

IOException

ClassNotFoundException

NoSuchMethodException

parse

public void parse()
           throws SQLException,
                  IOException,
                  ClassNotFoundException,
                  NoSuchMethodException

Specified by:

parse in class CellBaseParser

Throws:

SQLException

IOException

ClassNotFoundException

NoSuchMethodException

createSQLiteRegulatoryFiles

public void createSQLiteRegulatoryFiles(Path filePath,
                                        String tableName,
                                        List<String> columnNames,
                                        List<String> columnTypes)
                                 throws ClassNotFoundException,
                                        IOException,
                                        SQLException

Throws:

ClassNotFoundException

IOException

SQLException

getChromosomesList

public List<String> getChromosomesList(Path dbPath,
                                       String tableName)
                                throws IOException

Throws:

IOException

queryChromosomesRegulatoryDB

public List<org.opencb.biodata.models.core.RegulatoryFeature> queryChromosomesRegulatoryDB(Path dbPath,
                                                                                           String tableName,
                                                                                           String chromosome)

queryRegulatoryDB

public static List<org.opencb.biodata.models.core.RegulatoryFeature> queryRegulatoryDB(Path dbPath,
                                                                                       String tableName,
                                                                                       String chrFile,
                                                                                       int start,
                                                                                       int end)

getFields

public static List<String> getFields(String line,
                                     String tableName)

getAnnotatedFeaturesFields

@Deprecated
public static List<String> getAnnotatedFeaturesFields(String line)

Deprecated.

getRegulatoryFeaturesFields

public static List<String> getRegulatoryFeaturesFields(String line)

getMotifFeaturesFields

public static List<String> getMotifFeaturesFields(String line)

getMirnaFeaturesFields

public static List<String> getMirnaFeaturesFields(String line)

insertByType

public static void insertByType(PreparedStatement ps,
                                List<String> fields,
                                List<String> types)
                         throws SQLException

Throws:

SQLException

repeat

public String repeat(String s,
                     int n)